Projects in Awesome Lists by mskcc
A curated list of projects in awesome lists by mskcc .
https://github.com/mskcc/facets
Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
Last synced: 10 Mar 2026
https://github.com/mskcc/mutation-signatures
Create mutation signatures from MAF's, and decompose them into Stratton signatures
Last synced: 30 Apr 2025
https://github.com/mskcc/ngs-filters
Filters for false-positive mutation calls in NGS
Last synced: 30 Apr 2025
https://github.com/mskcc/lohhla
Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs
Last synced: 30 Apr 2025
https://github.com/mskcc/mimsi
Microsatellite Instability Classification using Multiple Instance Learning
cancer-genomics deep-learning genomics machine-learning multiple-instance-learning
Last synced: 30 Apr 2025
https://github.com/mskcc/roslin-variant
Roslin is a reproducible and reusable workflow for Cancer Genomic Sequencing Analysis
Last synced: 19 Jul 2025
https://github.com/mskcc/cbsp-hackathon
Computational Biology Summer Program Hackathon
Last synced: 30 Apr 2025
https://github.com/mskcc/tempo
CCS research pipeline to process WES and WGS TN pairs
Last synced: 30 Apr 2025
https://github.com/mskcc/facets2n
Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations
allele-specific copy-number-variation ngs ngs-analysis
Last synced: 08 Mar 2026
https://github.com/mskcc/innovation-impact-pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
Last synced: 30 Apr 2025
https://github.com/mskcc/marianas
Software for processing molecular barcoding (UMI)-based NGS data
Last synced: 06 Aug 2025
https://github.com/mskcc/access-pipeline
cfDNA Sequencing Pipeline with UMI
Last synced: 30 Apr 2025
https://github.com/mskcc/temposig
Fitting mutational catalog to signatures with maximum likelihood
Last synced: 23 Feb 2026
https://github.com/mskcc/cmo
Command-line tools for data analysts at the CMO
Last synced: 02 Sep 2025
https://github.com/mskcc/forte
Functional Observation of RNA Transcriptome Elements/Expression
Last synced: 28 Feb 2025
https://github.com/mskcc/hermes
Data collection management and analysis of information
Last synced: 30 Apr 2025
https://github.com/mskcc/vcf2tsv
a tool that takes the output files of different callers and creates maf-like, row-based output
Last synced: 08 Feb 2026
https://github.com/mskcc/medidata.rws.net
Medidata.RWS.NET is a comprehensive, fluent .NET API library for Medidata RAVE Web Services (RWS). It handles a large portion of the boilerplate C# code you'd normally have to write in order to communicate with RWS, allowing you to get up and running faster.
Last synced: 01 Mar 2026
https://github.com/mskcc/deepsig
Single-Base Substitution Mutational Signature Inference for WES and MSK-IMPACT
Last synced: 12 Feb 2026
https://github.com/mskcc/redcap-ddp-laravel
A Laravel implementation of the REDCap DDP (Dynamic Data Pull) middleware.
Last synced: 30 Apr 2025
https://github.com/mskcc/cwl-commandlinetools
Central location for CWL CommandLineTools
Last synced: 28 Feb 2025
https://github.com/mskcc/medidata.rws.net.standard
Medidata.RWS.NET.Standard is a comprehensive, fluent .NET Standard 2.0 API library for Medidata RAVE Web Services (RWS). It handles a large portion of the boilerplate C# code you'd normally have to write in order to communicate with RWS, allowing you to get up and running faster.
Last synced: 30 Apr 2025
https://github.com/mskcc/igo-lims-plugins
Sapio LIMS customizations to workflows for IGO
Last synced: 12 May 2025
https://github.com/mskcc/neoantigen-pipeline
Pipeline for computing neoantigen qualities from DNA and RNA-Seq data
Last synced: 16 Sep 2025
https://github.com/mskcc/waltz
Fast, efficient bam metrics, pileups and genotyping
Last synced: 28 Feb 2025
https://github.com/mskcc/igo-delivery
Delivery email, symlinks and permissions for IGO projects
Last synced: 10 Oct 2025
https://github.com/mskcc/helix_filters_01
Workflows for post-pipeline data processing and file generation
Last synced: 26 Oct 2025
https://github.com/mskcc/chl-spatial-profiling
Code supporting results of cHL manuscript
Last synced: 06 Feb 2026
https://github.com/mskcc/roslin-helix
Documentation for Roslin/Helix Pipeline
Last synced: 28 Jan 2026
https://github.com/mskcc/simba
Runs all thenextflow workflow scripts for IMPACT processing
Last synced: 25 Feb 2026
https://github.com/mskcc/fp-docker
Facets Preview Docker implementation for local use.
Last synced: 16 Jan 2026
https://github.com/mskcc/hera
First web app to be hosted on delphi.mskcc.org.
Last synced: 28 Feb 2025
https://github.com/mskcc/variant_launch_validation
a legacy project to validate m/p/g files
Last synced: 11 Aug 2025
https://github.com/mskcc/chronos
Generate uuid's that will sort chronologically
Last synced: 04 Jun 2026
https://github.com/mskcc/gdd-phase2
This is the Second Generation of Genome Derived Diagnosis AI Project
Last synced: 14 Aug 2025
https://github.com/mskcc/ngs-stats
NGS Statistics Database with historical Picard Stats, IGO fastq.gz paths and Sequencer Start & Stop Times
Last synced: 17 Jun 2025
https://github.com/mskcc/mskprotobuf
Repository for storing protocol buffer definitions and generated code
Last synced: 10 Apr 2026
https://github.com/mskcc/vcf_accuracy
vcf accuracy evaluator using VT, BEDTOOLS, PyVCF, and TABIX
Last synced: 18 Jun 2025
https://github.com/mskcc/awsbatch_mock
AWSBatch Mock built for scaling tests
Last synced: 03 Mar 2026
https://github.com/mskcc/smile-commons
Centralized configurations for checkstyle plugin and dependency management.
Last synced: 11 Dec 2025
https://github.com/mskcc/nf-fastq-plus
Generate IGO fastqs, bams, stats and fingerprinting
Last synced: 17 Jun 2026
https://github.com/mskcc/triassic
Containers to faciliate the running of old (pre-disaster) JUNO scripts
Last synced: 01 Mar 2026
https://github.com/mskcc/mjolnir-spec
Specification for the CI utility container
Last synced: 19 Mar 2026
https://github.com/mskcc/external-samples-rest
Rest service to retrieve DMP samples for IGO
Last synced: 03 Mar 2026
https://github.com/mskcc/rediscoverte
Pipeline for quantifying genome-wide TE expression in RNA sequencing data
Last synced: 03 Mar 2026
https://github.com/mskcc/natural-language-processing-with-deep-learning-in-healthcare
Last synced: 04 Mar 2026
https://github.com/mskcc/msk_impact_heme
Dataset analyzed for the 2022 MSK-IMPACT Heme Manuscript
Last synced: 04 Mar 2026
https://github.com/mskcc/mobius
Until we find a better name: umbrella term for Argos Next Step
Last synced: 05 Mar 2026
https://github.com/mskcc/toil-elk
Template for running Toil on LSF HPC with ELK stack logging
Last synced: 05 Mar 2026
https://github.com/mskcc/vepcheck
Nextflow pipeline to check different vep version
Last synced: 06 Mar 2026
https://github.com/mskcc/sample-metadata-app
An effort to make sample related metadata available through an API and a frontend to everyone inside MSKCC.
Last synced: 09 Jun 2026
https://github.com/mskcc/pi-manifest-autogen
Autogenerate manifest files to run pipeline
Last synced: 10 Jun 2026
https://github.com/mskcc/redcap-data-dictionary-diff
A tool for analyzing and displaying the differences between two REDCap data dictionaries. Outputs into an Excel spreadsheet.
Last synced: 11 May 2026
https://github.com/mskcc/ddp-spec-date-collector
Fetches clinical sample collection dates from ddp web service for given set of ids
Last synced: 11 May 2026
https://github.com/mskcc/agreto
Find wild-type sequences of neoantigens and run netMHCpan
Last synced: 11 May 2026